A couple things to think about:
It's not cheap. You pay for the car, ticket per person & room upgrades. But it is more economical the more people you have in the room.
If you're traveling with folks who need to move around or go to the bathroom frequently, the autotrain is ideal since the train keeps traveling. No need for those pesky refueling stops. 
Now if you have one of the downstairs family rooms with it's own bathroom this isn't an issue, but if you're in a roomette or coach you'll be using the shared facilities... which are tiny like airplane toilets. Not an ideal situation for Pooh-Sized folks. 
Remember you will be on a rocking, moving vehicle. This can keep some people awake. Also it makes walking the halls interesting. For those with mobility issues you can have your meals brought to you.
On the plus side, I was surprised how comfortable the roomette beds were. Also the rooms & roomettes have electrical outlets. (But there was no Wifi on the train when I took it 2010.)
If you have a seat on the east-side of the train you can see the Fredericksburg pyramid.
Now for Harry Potter fans there is one great big plus - you can say you took an Express train to Hogwarts! (Which is why I did it for my first trip to WWoHP. )